Add nodes to a custom node tree
The example of the custom PyNode tree includes information about how to add nodes to the menus via NodeCategory so i'm going to assume you've got menus working. 

(if not: see TextEditor > Templates > Python > Custom Nodes )

If you want to add a node via python, it's the same as with shader trees or compositor trees, except you use data.node_groups.

ng = bpy.data.node_groups['MyNodeTree']
new_node = ng.nodes.new(your_nodes_bl_idname)
new_node.location = (20, 40)